[med-svn] [ariba] 05/14: adjust patches

[Sascha Steinbiss]

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satta pushed a commit to branch master
in repository ariba.

commit c36464316a076b42864974fb7c9c0e2cc3efca80
Author: Sascha Steinbiss <satta at debian.org>
Date:   Sun Jul 31 18:11:45 2016 +0000

    adjust patches
---
 debian/patches/fix-spades-call.patch |  2 +-
 debian/patches/rename-cdhit.patch    | 30 +++++-------------------------
 debian/patches/series                |  2 --
 3 files changed, 6 insertions(+), 28 deletions(-)

diff --git a/debian/patches/fix-spades-call.patch b/debian/patches/fix-spades-call.patch
index 9ee6afa..6acc01f 100644
--- a/debian/patches/fix-spades-call.patch
+++ b/debian/patches/fix-spades-call.patch
@@ -7,7 +7,7 @@ Description: fix SPAdes call
 Author: Sascha Steinbiss <satta at debian.org>
 --- a/ariba/external_progs.py
 +++ b/ariba/external_progs.py
-@@ -69,8 +69,8 @@
+@@ -72,8 +72,8 @@
              # python3.4, not python2. SPAdes throws an error about not being
              # compatible with python3.4.
              # This means we need to explicitly run SPAdes with python2.
diff --git a/debian/patches/rename-cdhit.patch b/debian/patches/rename-cdhit.patch
index 68339b1..dc9f13a 100644
--- a/debian/patches/rename-cdhit.patch
+++ b/debian/patches/rename-cdhit.patch
@@ -3,34 +3,14 @@ Description: use Debian name for CD-HIT
 Author: Sascha Steinbiss <satta at debian.org>
 --- a/ariba/external_progs.py
 +++ b/ariba/external_progs.py
-@@ -12,7 +12,7 @@
+@@ -12,8 +12,8 @@
  prog_to_default = {
      'bcftools': 'bcftools',
      'bowtie2': 'bowtie2',
 -    'cdhit': 'cd-hit-est',
+-    'cdhit2d': 'cd-hit-est-2d',
 +    'cdhit': 'cdhit-est',
-     'gapfiller': 'GapFiller.pl',
++    'cdhit2d': 'cdhit-est-2d',
+     #'gapfiller': 'GapFiller.pl',
+     'mash': 'mash',
      'nucmer' : 'nucmer',
-     'samtools': 'samtools',
---- a/ariba/cdhit.py
-+++ b/ariba/cdhit.py
-@@ -15,7 +15,7 @@
-       threads=1,
-       length_diff_cutoff=0.9,
-       verbose=False,
--      cd_hit_est='cd-hit-est',
-+      cd_hit_est='cdhit-est',
-       rename_suffix='x',
-     ):
- 
---- a/ariba/reference_data.py
-+++ b/ariba/reference_data.py
-@@ -459,7 +459,7 @@
-         pyfastaq.utils.close(f_out)
- 
- 
--    def cluster_with_cdhit(self, inprefix, outprefix, seq_identity_threshold=0.9, threads=1, length_diff_cutoff=0.9, nocluster=False, verbose=False, cd_hit_est='cd-hit-est', clusters_file=None):
-+    def cluster_with_cdhit(self, inprefix, outprefix, seq_identity_threshold=0.9, threads=1, length_diff_cutoff=0.9, nocluster=False, verbose=False, cd_hit_est='cdhit-est', clusters_file=None):
-         files_to_cat = []
-         clusters = {}
- 
diff --git a/debian/patches/series b/debian/patches/series
index 22823e7..11fb5eb 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,3 +1 @@
 rename-cdhit.patch
-fix-spades-call.patch
-relax-pysam-version.patch

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